Dichroism measurement

Infrared, nuclear magnetic resonance, ultraviolet, optical rotary dispersion and circular dichroism measurements have been used for the spectral analysis of thiiranes. A few steroidal thiiranes have been reported to possess infrared absorption in the range from 580 to 700 cm The intermediate thiocyanate derivatives (RSCN) have a strong sharp peak at 2130-2160 cm the isomeric isothiocyanate (RNCS) shows a much stronger but broad band at 2040-2180 cm. ... 

For example, infra-red dichroism measurements will give a value for . If the direction of dipole moment change for the vibration under consideration makes an angle S, with the chain axis, the average for the chain distribution in 0 relates to by the simple relationship... 

Circular Dichroism Measurements. The absolute configurations of the C6 chiral center in tetrahydrobiopterin cofactor and related compounds were determined by comparison of their circular dichroism (CD) spectra with those of... 

Compounds 167-171 outlined in Fig. 43 form another series of diboronic acids that form complexes with mono- and disaccharides. In these cases the asymmetrical immobilization of chromophoric functional groups, e.g., aromatic rings in 167-170 or Fe -complexation with the related boronate 171, can be analyzed by circular dichroism measurements [256-262]. 

Fig. 43. Compounds 167-171 form a series of diboronic acids for the complexation of saccharides with functional groups that permit analysis by circular dichroism measurements...

The classical scheme for dichroism measurements implies measuring absorbances (optical densities) for light electric vector parallel and perpendicular to the orientation of director of a planarly oriented nematic or smectic sample. This approach requires high quality polarizers and planarly oriented samples. The alternative technique [50, 53] utilizes a comparison of the absorbance in the isotropic phase (Dj) with that of a homeotropically oriented smectic phase (Dh). In this case, the apparent order parameter for each vibrational oscillator of interest S (related to a certain molecular fragment) may be calculated as S = l-(Dh/Di) (l/f), where / is the thermal correction factor. The angles of orientation of vibrational oscillators (0) with respect to the normal to the smectic layers may be determined according to the equation... 

The IR dichroism measurements allowed a fairly precise determination of the preferential molecular conformations both in the smectic Ai and X phases (see Sect. 2.3). In the smectic Ai phase the biphenyl moiety is parallel on average to the layer normal, while the hydrocarbon and perfluorinated fragments are tilted at angles 18 and 32°, respectively. The phase transition to the smectic X phase is accompanied by a dramatic change in the main molecular conformation - now all the fragments are strongly tilted with respect to the layer normal (especially the biphenyl core which tilts at an angle of around 56°) (Fig. 12). 

Of course, it is possible to contemplate experiments that examine photoionization of oriented chiral molecules. An expression has been given for the angle integrated (total) ionization cross-section in such circumstances [48] and CDAD-type measurements have been reported on adsorbed chiral molecules [49, 50], but the interplay of natural and geometric chirality in angle-resolved dichroism measurements remains very much a topic for future investigation. 

Unfortunately, in the VUV region no polarimetry data are available, but calculations indicate the degree of circular polarization achieved by the wiggler may be 80%, estimated to be no worse than 70% delivered at the experimental chamber [95, 96]. In PECD experiments, we have calibrated the polarization state by deduction from cross-comparison of results at a few fixed energies previously studied on the SU5 beamline where accurate polarimetry data was available [36]. Because the horizontal magnetic field array in the insertion device is electromagnetic, fast current reversal to switch left- and right-handed elliptical polarizations is possible, with the usual potential benefit for dichroism measurements. 

The conformational changes which have been described so far are probably all relatively small local changes in the structure of H,K-ATPase. This has been confirmed by Mitchell et al. [101] who demonstrated by Fourier transform infrared spectroscopy that a gross change in the protein secondary structure does not occur upon a conformational change from Ei to 3. Circular dichroism measurements, however [102,103], indicated an increase in a-helical structure upon addition of ATP to H,K-ATPase in the presence of Mg and... 

The non-covalently bound BPDEs to DNA formed initially appear to be intercalation complexes (1 6,52-55) Meehan et al. (1 6) report that the BPDE intercalates into DNA on a millisecond time scale while the BPDE alkylates DNA on a time scale of minutes. Most of the BPDE is hydrolyzed to tetrols (53-56). Geacintov et al. (5l ) have shown with linear dichroism spectral measurements that the disappearance of intercalated BPDE l(+) is directly proportional to the rate of appearance of covalent adducts. These results suggest that either there may be a competition between the physically non-covalently bound BPDE l(+) and an externally bound adduct or as suggested by the mechanism in the present paper, an intercalative covalent step followed by a relaxation of the DNA to yield an externally bound adduct. Their results for the BPDE i(-) exhibit both intercalative and externally bound adducts. The linear dichroism measurements do not distinguish between physically bound and covalent bound forms which are intercalative in nature. Hence the assumption that a superposition of internal and external sites occurs for this isomer. 

The linear dichroism measurement demonstrated that MOPPV chains formed the planar orientation chains in the LB films dichroic ratio Ap/As... 

Circular dichroism measurements on soluble Sup35pN and NM domains indicate a largely unfolded structure (Glover et al, 1997 King et al., 1997). 

Circular Dichroism Measurements. Circular dichroism measurements were carried out by using a Cary model 6002 spectro-polarimeter calibrated with d-10 camphor sulfonic acid. All measurements were run at room temperature in the same 1 cm, quartz cell over the near-ultraviolet region (250-330 nm). 

Figure 19.1. Schematic diagram of a general pump-probe-detect laser spectrometer suitable for picosecond electronic absorption, infrared (IR) absorption, Raman, optical calorimetry, and dichroism measurements. For picosecond fluorescence—a pump-detect method, no probe pulse needs to be generated.

If two different three-dimensional arrangements in space of the atoms in a molecule are interconvertible merely by free rotation about bonds, they are called conformations if not, configurations.l85 Configurations represent isomers that can be separated, as previously discussed in this chapter. Conformations represent conformers, which are rapidly interconvertible and thus nonseparable. The terms conformational isomer and rotamer are sometimes used instead of conformer. A number of methods have been used to determine conformations.186 These include x-ray and electron diffraction, ir, Raman, uv, nmr,187 and microwave spectra,188 photoelectron spectroscopy,189 supersonic molecular jet spectroscopy,190 and optical rotatory dispersion and circular dichroism measurements.191 Some of these methods are useful only for solids. It must be kept in mind that the conformation of a molecule in the solid state is not necessarily the same as in solution.192 Conformations can be calculated by a method called molecular mechanics (p. 149). 

In fact Schulz and co-workers (131,134), and Klabunovskii, Shvartsman and Petrov (55) report that the O. R. D. curves of poly-menthyl-acrylate, poly-bornyl-acrylate and poly-2-methyl-butyl-methacrylate show a maximum at about 300 mp, the wavelength corresponding to the maximum being related to the method of preparation of the polymer. Circular dichroism measurements seem advisable in order to confirm the existence of a Cotton effect postulated by the above authors in that wavelength range. 

The method is less powerful in characterizing proteins lacking tryptophan, for reasons mentioned earlier (see Support Protocol), and does not apply at all to the rare proteins that lack tyrosine as well. Near-UV circular dichroism measurements (unit 7.6) can still be of considerable value for proteins containing tyrosine and, in both cases, both far-UV circular dichroism and urea-gradient gel electrophoresis (unit 7.4) provide powerful contributions to characterization. 

Nuclease behaves like a typical globular protein in aqueous solution when examined by classic hydrodynamic methods (40) or by measurements of rotational relaxation times for the dimethylaminonaphth-alene sulfonyl derivative (48)- Its intrinsic viscosity, approximately 0.025 dl/g is also consistent with such a conformation. Measurements of its optical rotatory properties, either by estimation of the Moffitt parameter b , or the mean residue rotation at 233 nin, indicate that approximately 15-18% of the polypeptide backbone is in the -helical conformation (47, 48). A similar value is calculated from circular dichroism measurements (48). These estimations agree very closely with the amount of helix actually observed in the electron density map of nuclease, which is discussed in Chapter 7 by Cotton and Hazen, this volume, and Arnone et al. (49). One can state with some assurance, therefore, that the structure of the average molecule of nuclease in neutral, aqueous solution is at least grossly similar to that in the crystalline state. As will be discussed below, this similarity extends to the unique sensitivity to tryptic digestion of a region of the sequence in the presence of ligands (47, 48), which can easily be seen in the solid state as a rather anomalous protrusion from the body of the molecule (19, 49). 

In the following we will compare the order parameter of the dve u Table 4) which is an azoderivative, dissolved in the 1-l.c. (M2 in Table 4) andtT Id in the side chain polymer (M3), which has a very similar chemical Issove to the 1-l.c.57). The linear dichroism measurements for the polymer/d°nSt,tUt,°n M3, is shown in Fig. 13, measured at X = 430 nm, which is the absorptiony ShStdm,... 

Using this method in Fig. 15, the order parameters vs. temperature of the polymers are compared with the corresponding monomer mixture Ml. The monomer Ml exhibits a higher value of S than the polymer by about 10 % and confirms the previous linear dichroism measurements. If we compare the magnitude and temperature dependence of S for the polymers Cl to C3, which differ in the length of the flexible spacer, no difference in S can be found within the experimental error. 

Well organized Langmuir-Blodgett (LB) films have been obtained from mixtures of a push-pull carotenoid and co-tricosenoic acid as shown in 7. These mixed films exhibit a very good cohesion, with an area of about 25 A2 per carotenoid molecule. They can easily be transferred onto solid substrates. Examination by UV-visible linear dichroism measurements confirms that the carotenoid chains are oriented perpendicularly to the surface of the substrate in card-packed aggregates, in which the polyenic chains interact via excitonic coupling, as indicated by the large hypsochromic shift of the tc-tc transition (20). 

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